Lab Meeting (12-01-2017)

Ming Chen

12/01/2017

Overview

Singularity Container

What can container technologies do for you?

Singularity Container

Building containers

Singularity Container

What is cool about Singularity container?

Singularity Container

Demo

Get Singularity ready on my local computer

mkdir -p ~/Desktop/singularity-images && cd ~/Desktop/singularity-images
docker run -it --rm --privileged -v ~/Desktop/singularity-images:/home/singularity-images mingchen0919/docker-singularity

Pull a container with R installed to my local computer.

cd /home/singularity-images
singularity build --writable r.img docker://r-base

Run the R container

# check the image file
ls 

# run container interactively
singularity shell --writable r.img

Test that the R package plyr does not exist before we install it

R
require('plyr')

Install package plyr

install.packages('plyr')
require('plyr')

Exit the singularity container

exit

Transfer the container to a HPC cluster

scp r.img  mchen33@149.165.156.175:/home/mchen33/r.img

Run the container on the HPC cluster as non-root user.

# login to the HPC cluster
ssh mchen33@149.165.156.175

singularity shell r.img

# check the testing package
R
require('plyr')

Tripal Galaxy and Galaxy workflows

How biologists (who have very limited programming experience) can use Galaxy to perform bioinformatics analysis (Demo)

Tripal Galaxy and Galaxy workflows

Launch a Galaxy instance with Docker

We are going to use the Docker container created by Björn Grüning.

Launch a docker container which has galaxy installed

docker run -it --rm --name=galaxy_instance \
        -p 80:80 -p 8021:21 -p 8022:22 \
        -e "ENABLE_TTS_INSTALL=True" \
        -e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
        bgruening/galaxy-stable:17.01 /bin/bash

Start Galaxy

startup

Tripal Galaxy and Galaxy workflows

Tripal Galaxy and Galaxy workflows

Run Galaxy workflows from a Tripal site with Tripal Galaxy module

Updates on R Markdown Galaxy tools

What is a Galaxy tool?

Updates on R Markdown Galaxy tools

What is an R Markdown Galaxy tool?

Updates on R Markdown Galaxy tools

How R Markdown benefits the development of Galaxy tools?

Updates on R Markdown Galaxy tools

Templates available for developing R Markdown Galaxy tools

Updates on R Markdown Galaxy tools

R Markdown Galaxy tools on Tool Shed

Galaxy Tool Generator platform

Galaxy Tool Generator (GTG) is a web-based platform for asisting Galaxy tool development. The components of the GTG platform includes:

Galaxy Tool Generator platform

What GTG platform can do?

Galaxy Tool Generator platform

Start GTG platform

The platform is still under development. The code below will eventually replaced by a one line command.

mkdir -p ~/Desktop/galaxy-tool-generator-dev && cd ~/Desktop/galaxy-tool-generator-dev
git clone https://github.com/MingChen0919/galaxy_tool_generator.git
git clone https://github.com/MingChen0919/galaxy_tool_generator_ui.git
git clone https://github.com/galaxyproject/blend4php.git

docker run -it -p 8090:80 --rm --network=galaxy_tool_generator_nw \
            -v $(pwd)/galaxy_tools:/var/www/html/sites/default/files/galaxy_tools \
            -v $(pwd)/galaxy_tool_generator:/var/www/html/sites/all/modules/galaxy_tool_generator \
            -v $(pwd)/galaxy_tool_generator_ui:/var/www/html/sites/all/modules/galaxy_tool_generator_ui \
            -v $(pwd)/blend4php:/var/www/html/sites/all/libraries/blend4php \
            mingchen0919/docker-galaxy-tool-generator '/bin/bash'
   
drush en -y galaxy_tool_generator galaxy_tool_generator_ui

Go to http://127.0.0.1:8090/

Galaxy Tool Generator platform

Create Galaxy tools (demo)

Galaxy Tool Generator platform

Publish to Tool Shed/Test Tool Shed

See https://testtoolshed.g2.bx.psu.edu/ and search for test_galaxy_tool_generator.

Galaxy Tool Generator platform

Install and test tool on a Galaxy instance

cd ~/Desktop/galaxy-tool-generator-dev && mkdir shed_tools
 
docker run -it --rm --network=galaxy_tool_generator_nw --name=galaxy_instance \
        -p 8080:80 -p 8021:21 -p 8022:22 \
        -v $(pwd)/shed_tools:/export/shed_tools \
        -e "ENABLE_TTS_INSTALL=True" \
        -e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
        bgruening/galaxy-stable:17.01 /bin/bash
startup